CRISPR Screen Dataset

Aguirre AJ (2016) - 17-PMID27260156

H. sapiens

Title: Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.

Screen Rationale : Cell-essential genes
Cell Type : Cancer Cell Line [EFO:0001639]
Cell Line : MHH-ES-1 [EFO:0006650, CELLOSAURUS:CVCL_1411]
Phenotype : Cell Proliferation
Library : GECKO v2 [AddGene] | Type: CRISPRn | Format: Pool | Enzyme: Cas9 | Methodology: Knockout
Analysis Method : CERES | Number of Hits: 1,870 | Full Dataset Size: 17,627
Experimental Setup : Timecourse | Duration: 21 Days | MOI: < 1
Significance : Authors have indicated that results with Score.2 (FDR) < 0.05 are to be considered significant. These results are indicated by 'Yes' in the HIT column of the table below.

The 33 cell line GeCKOv2 dataset from PMID:27260156 was re-analysed using the CERES method in PMID:29083409 and this CERES dataset was loaded into ORCS. To identify gene hits at an FDR < 0.05, ORCS estimated FDRs for the CERES GeCKOv2 dataset using customized gold-standard positive and negative sets of genes. The custom positive set included genes essential in at least 90% of cell lines in both the CERES Avana dataset (PMID:29083409) and the 10 cell lines included in Bertomeu et al. (PMID:29038160). The custom negative set included genes essential in zero cell lines from one of the two datasets and in <=10% of the other dataset. Genes scoring among the top 1,500 in >10% and at least two cell lines in either of the following three studies were further filtered from the negative set: PMID:27260156, PMID:27760321, PMID:28162770.

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